Fine Mapping and Candidate Gene Analysis of Small Round Grain Mutant in Rice

Grain size and panicle architecture are important traits determining yield. Here we report a new allele of DEP2 (dense and erect panicle 2) which has a pleiotropic effect on grain size/shape and panicle architecture. A small round grain and erect panicle mutant was obtained by treating japonica cultivar Hwacheong waxy with MNU (N-methyl-N-nitrosourea). Through fine mapping sequence analysis, we identified the single nucleotide substitution in the mutant, which caused splicing error of the first intron, on previously reported DEP2 locus in rice. Since the dep2-1 and dep2-2 have been reported in previous studies, we named this new allele as dep2-3. The dep2-3 mutant manifested reduced grain size and plant height, dense and erect panicle and erect plant architecture. When we crossed the mutant with wild type, panicle and grain of F1 plant showed intermediate phenotype, indicating that dep2-3 showed incomplete dominance, which was not reported in the previous study. Scanning electron microscopy (SEM) results showed that increase in width of mutant grain was due to the increased width of glume cells. Paraffin section of peduncle revealed that outgrowth in outer layer of peduncle compared to inner layer caused the erectness of the panicle. Our results collectively indicated that the dep2-3 might play a significant role in the regulation of grain size/shape and formation of vascular bundles.